Hi Justin,<br><br>When i define <br><br><pre>define = FLEXIBLE <br> constraints = none<br> constraint-algorithm = Lincs<br></pre><br><br>I saw my .log file. <br><div></div><br>Input Parameters:<br> integrator = md<br> nsteps = 10000<br> init_step = 0<br> ns_type = Grid<br> nstlist = 5<br> ndelta = 2<br> nstcomm = 1<br> comm_mode = Linear<br> nstlog = 50<br> nstxout = 0<br> nstvout = 0<br> nstfout = 0<br> nstenergy = 50<br> nstxtcout = 50<br> init_t = 0<br> delta_t = 0.002<br> xtcprec = 1000<br> nkx = 0<br> nky = 0<br> nkz = 0<br> pme_order = 4<br> ewald_rtol = 1e-05<br> ewald_geometry = 0<br> epsilon_surface = 0<br> optimize_fft = FALSE<br> ePBC = xyz<br> bPeriodicMols = FALSE<br> bContinuation = FALSE<br> bShakeSOR = FALSE<br> etc = Berendsen<br> epc = Berendsen<br> epctype = Isotropic<br> tau_p = 0.5<br> ref_p (3x3):<br> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}<br> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}<br> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}<br> compress (3x3):<br> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}<br> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}<br> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}<br> refcoord_scaling = No<br> posres_com (3):<br> posres_com[0]= 0.00000e+00<br> posres_com[1]= 0.00000e+00<br> posres_com[2]= 0.00000e+00<br> posres_comB (3):<br> posres_comB[0]= 0.00000e+00<br> posres_comB[1]= 0.00000e+00<br> posres_comB[2]= 0.00000e+00<br> andersen_seed = 815131<br> rlist = 0.9<br> rtpi = 0.05<br> coulombtype = Cut-off<br> rcoulomb_switch = 0<br> rcoulomb = 0.9Input Parameters:<br> integrator = md<br> nsteps = 10000<br> init_step = 0<br> ns_type = Grid<br> nstlist = 5<br> ndelta = 2<br> nstcomm = 1<br> comm_mode = Linear<br> nstlog = 50<br> nstxout = 0<br> nstvout = 0<br> nstfout = 0<br> nstenergy = 50<br> nstxtcout = 50<br> init_t = 0<br> delta_t = 0.002<br> xtcprec = 1000<br> nkx = 0<br> nky = 0<br> nkz = 0<br> pme_order = 4<br> ewald_rtol = 1e-05<br> ewald_geometry = 0<br> epsilon_surface = 0<br> optimize_fft = FALSE<br> ePBC = xyz<br> bPeriodicMols = FALSE<br> bContinuation = FALSE<br> bShakeSOR = FALSE<br> etc = Berendsen<br> epc = Berendsen<br> epctype = Isotropic<br> tau_p = 0.5<br> ref_p (3x3):<br> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}<br> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}<br> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}<br> compress (3x3):<br> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}<br> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}<br> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}<br> refcoord_scaling = No<br> posres_com (3):<br> posres_com[0]= 0.00000e+00<br> posres_com[1]= 0.00000e+00<br> posres_com[2]= 0.00000e+00<br> posres_comB (3):<br> posres_comB[0]= 0.00000e+00<br> posres_comB[1]= 0.00000e+00<br> posres_comB[2]= 0.00000e+00<br> andersen_seed = 815131<br> vdwtype = Cut-off<br> rvdw_switch = 0<br> rvdw = 0.9<br> epsilon_r = 1<br> epsilon_rf = 1<br> tabext = 1<br> implicit_solvent = No<br> gb_algorithm = Still<br> gb_epsilon_solvent = 80<br> nstgbradii = 1<br> rgbradii = 2<br> gb_saltconc = 0<br> gb_obc_alpha = 1<br> gb_obc_beta = 0.8<br> gb_obc_gamma = 4.85<br> sa_surface_tension = 2.092<br> DispCorr = EnerPres<br> free_energy = no<br> init_lambda = 0<br> sc_alpha = 0<br> sc_power = 0<br> sc_sigma = 0.3<br> delta_lambda = 0<br> nwall = 0<br> wall_type = 9-3<br> wall_atomtype[0] = -1<br> wall_atomtype[1] = -1<br> wall_density[0] = 0<br> wall_density[1] = 0<br> wall_ewald_zfac = 3<br> pull = no<br> disre = No<br> disre_weighting = Conservative<br> disre_mixed = FALSE<br> dr_fc = 1000<br> dr_tau = 0<br> nstdisreout = 100<br> orires_fc = 0<br> orires_tau = 0<br> nstorireout = 100<br> dihre-fc = 1000<br> em_stepsize = 0.01<br> em_tol = 100<br> niter = 20<br> fc_stepsize = 0<br> nstcgsteep = 1000<br> nbfgscorr = 10<br> ConstAlg = Lincs<br> shake_tol = 0.0001<br> lincs_order = 4<br> lincs_warnangle = 30<br> lincs_iter = 1<br> bd_fric = 0<br> ld_seed = 1993<br> cos_accel = 0<br> deform (3x3):<br> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> userint1 = 0<br> userint2 = 0<br> userint3 = 0<br> userint4 = 0<br> userreal1 = 0<br> userreal2 = 0<br> userreal3 = 0<br> userreal4 = 0<br>grpopts:<br> nrdf: 1941<br> ref_t: 300<br> tau_t: 0.1<br>anneal: No<br>ann_npoints: 0<br> acc: 0 0 0<br> nfreeze: N N N<br> energygrp_flags[ 0]: 0<br> efield-x:<br> n = 0<br> efield-xt:<br> n = 0<br> efield-y:<br> n = 0<br> efield-yt:<br> n = 0<br> efield-z:<br> n = 0<br> efield-zt:<br> n = 0<br> bQMMM = FALSE<br> QMconstraints = 0<br> QMMMscheme = 0<br> scalefactor = 1<br>qm_opts:<br> ngQM = 0<br>Table routines are used for coulomb: FALSE<br>Table routines are used for vdw: FALSE<br>Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9<br>System total charge: 0.000<br><br>Enabling SPC water optimization for 216 molecules.<br><br>Configuring nonbonded kernels...<br>Testing AMD 3DNow support... not present.<br>Testing ia32 SSE support... present.<br><br><br><br><br><br><br><br><br><br><br><br><br><br>However if i <br><pre>define =<br><br>constraints = none<br>constraint-algorithm = Lincs<br><br>The .log file is similar to the above .log file. So i can not know whether the constraints invoked.<br><br><br>Is it only SETTLE algorithm for water models in Gromacs 4.5.3? </pre><pre><br>>
>
>MD wrote:
>> Hi gromacs experts,
>>
>> I used gromacs 4.5.3. my system has only spce water, no other types.
>>
>> In .mdp file,
>>
>> I used the following parameters;
>>
>> define =
>>
>> constraints = none
>> constraint-algorithm = Lincs
>>
>> Can u tell me Is it flexible water or all the bond, angle fixed using
>> the above setting?
>>
>
>Look at spce.itp and/or your md.log file. If the #ifdef FLEXIBLE statement is
>not invoked, the SETTLE algorithm is used.
>
>>
>> what is the equations of potential energy in Gromacs 4.5 using OPLSAA?
>>
>
>The components of various functional forms are described in the manual.
>
>-Justin
>
>>
>> Best regards
>>
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